Because polycyclic aromatic hydrocarbons (PAHs) and polybrominated diphenylethers (PBDEs) are ubiquitous and coexist in the environment and in wildlife, there are potential interactions between them that could cause toxic effects. In this study, the modulating effects of 2,2',4,4'-tetrabromodiphenyl ether (BDE47) and benzo[a]pyrene (BaP)-induced reproductive and developmental toxic effects in Japanese medaka (Oryzias latipes) were investigated by exposing adult Japanese medaka to BaP alone, BDE47 alone, and coexposing them with both BaP and BDE47 at different concentrations, respectively. Exposure to BaP alone significantly suppressed fecundity and egg protein content and markedly induced skeletal deformation in F1 generation eleutheroembryos. BDE47 significantly recovered reproductive functions, fecundity, and egg protein content, suppressed by BaP when the concentration of BDE47 increased to 0.44 μg/L. Such effects can be at least partly explained by the decreased BaP levels in the coexposure groups and the accompanying increase in the circulating level of 17β-estradiol in female medaka fish. The prevalence of skeletal deformations markedly increased to 19.3 ± 2.4% and 16.0 ± 1.6% in fish coexposed to BaP and BDE47 at 0.44 and 2.58 μg/L compared with that of fish exposed to 1.21 μg/L BaP alone (9.7 ± 1.7%), and the impacts on male medaka fish in the coexposure groups would be the crucial reason leading to these effects. Considering that the measured water concentrations of BaP and BDE47 in the present study were comparable with those reported in rivers and harbors, BaP and BDE47 contamination in the real world would have a significant level of interactive effects on wild fish.